[BiO BB] (no subject)

Indraneel Majumdar indraneel at indialine.org
Tue Sep 25 23:58:02 EDT 2001

Hi Val,

Sorry for the very late followup. After your mail I realised that truly
we are basing most of our bioinfo ideas on things like homology/analogy
rather than in terms of biochemical pathways, protein function prediction
in terms of cellular requirements and such things (something that I
wanted to do when I first entered this field, but lost sight of and
forgot very soon).

I believe the concepts you point out are at present fairly complicated
to represent and visualise using current software. Remember that most of
current software was generated not to study the unknown diversity but to
store man made discrete units (eg financial data). Possibly a giant step
is required to produce such things and since I cannot at present see any
necessity for it in the commercial world (since a .com will always want
quick results), such a system will most probably be an open source

Coming to the development issue, such software would require highly
experienced biologists to develop (maybe not highly, but at least a
person interested in Biology). Most people I have come across
interested in bioinformatics are from a non Biology background (there is
nothing wrong in that, this is a field where all need to contribute
from the viewpoint of his/her own specialisation). Thus the diversity is
either missed completely, or avoided because it's too complex. The few
biologists on this bandwagon do their best to forget (or as in my
case have already forgot) things like the evolution of the endocrine
hormone system, development of the inner ear, functioning of the lambda
genome (and such things).

The "parts" (that we study now) indeed make up the "whole", but we also
need to remember, maybe according to "chaos" (or the gaia hypothesis?),
that the whole is something more than just the parts.

On Sat, Sep 15, 2001 at 09:41:34PM -0400, Val Bykoski wrote:
> Hi Indraneel,
>     Thanx for your comments.
>     I refer to the cell as a biological cell, and my point,
>     to put it a little differently, was that data has to work
>     inside a (realistic) cell model, not to sit passively in databases.
>     Data grouping, visualization, etc. is better than nothing,
>     but still there is a huge gap between data (nicely grouped, 
>     visualized, etc) and their biological significance or context.
>     I guess my point is that if you integrate data into a realistic 
>     cell model, the model is both a predictive framework and 
>     a (bio)context-sensitive database for the data.  Then,
>     data is hidden and work inside the model for predictions,
>     and does not require grouping, visualization, etc.
>     Sure, the "realistic cell model" is a hard nut...but may be
>     worth of efforts, in particular, for a data-driven model.
> cheers, val
> val at vtek.com


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